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2 Answers
2

I believe the following theory, but I have never tried to back them up with an evidence:

It originates from a slang 中坊 (ちゅうぼう). It means “junior high student,” but often with an indication that the speaker looks down on the student he/she is talking about. (The usual word for “junior high student” is 中学生.)

On a BBS, calling someone 中坊 would be just another way to insult the person who is referred to; because the speaker does not know the age of the person referred to, it can only mean that the speaker thinks the action of the other party is childish as if he/she were a junior high student. But because 中坊 is a slang, popular IMEs cannot translate ちゅうぼう to 中坊. Because of this, the word 厨房 (kitchen) with the same pronunciation but completely unrelated meaning was used in place of 中坊 on a BBS. Later the abbreviation 厨 came into use.

ニコ厨 means a childish Niconico Video freak, and 東方厨 means a childish freak of games and/or game characters made by Touhou Project. But the meaning “childish” is sometimes ignored and they are often used to just refer to a Niconico Video freak or a Touhou Project freak.

Also it may be worth noting that ニコ厨 has the same pronunciation as ニコ中, which is an old-fashioned abbreviation for ニコチン中毒 (“dependence on nicotine/smoking”), and therefore ニコ厨 may be a pun for some people. But I do not know if this fact played any role in the etymology of the word ニコ厨.

@Dave: I posted it because in my opinion, it is an educated guess and it is not noise. If you downvoted it because it does not contain an evidence, it is fine, but whether it is a noise or not is a subjective matter.
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Tsuyoshi ItoJun 1 '11 at 5:44

Personally, I like to assume that ニコ中 comes from 自己中 :-)
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YOUJun 1 '11 at 5:57

@Dave: If the asker or someone else wants to, he/she can try to find evidences for what I wrote here. But if you want to keep saying that this answer is a noise, I am fine.
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Tsuyoshi ItoJun 1 '11 at 5:59

@Dave 中坊 is a short form for 中学生の坊主, which means "middle-schooler lad" in British English, or "middle grade lil' fella" in American. Because it is a slang, it's very difficult to find trustworthy source for its etymology. If it was internet slang, the definition could be found in databases like Hatena Keyword. But if it originated from offline subculture, it becomes more difficult to determine. @YOU 自己中 is from 自己中心, note the difference. @Ito I spy with my little eye, I spot a ニコ厨 lurking here…
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syockitJun 3 '11 at 19:45

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@Dave: I just provided what I could provide hoping that it would be useful to someone. What I wrote here is likely to be a mixture of what I read on the internet and what I guessed, and it is unclear to me which part is which. I thought that my evidence-less answer might be useful because I imagined that some people would have no clue where to start looking at. And you keep claiming that my post is a noise. How nice. Do not worry, I will not try to post any noise to your questions.
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Tsuyoshi ItoJun 7 '11 at 4:15